The Role of ncRNA in Centromeres: A Lesson from Marsupials

O’Neill, Rachel J.; Carone, Dawn M.

doi:10.1007/978-3-642-00182-6_4

Cited by 21 publications

(12 citation statements)

References 103 publications

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“…Studies from numerous organisms with point, regional or holocentric centromeres now point to the central importance of balanced transcription for centromere regulation, whether it is implicated in regulation of kinetochore assembly or in the assembly of pericentric heterochromatin that influences chromosome segregation efficiency (O’Neill and Carone 2009, Chueh et al 2009; Ohkuni and Kitagawa 2011; Gassmann et al 2012; Chan et al 2012). Recent work from the Verma lab has beautifully illustrated the importance of the tumor suppressor BRCA1 for assembly of heterochromatin in mammals (Zhu et al 2011).…”

Section: How Conserved Is the Process Of Heterochromatin Assembly At mentioning

confidence: 99%

Centromeric heterochromatin assembly in fission yeast—balancing transcription, RNA interference and chromatin modification

2012

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Distinct regions of the eukaryotic genome are packaged into different types of chromatin, with euchromatin representing gene rich, transcriptionally active regions and heterochromatin more condensed and gene poor. The assembly and maintenance of heterochromatin is important for many aspects of genome control, including silencing of gene transcription, suppression of recombination, and to ensure proper chromosome segregation. The precise mechanisms underlying heterochromatin establishment and maintenance are still unclear, but much progress has been made towards understanding this process during the last few years, particularly from studies performed in fission yeast. In this review, we hope to provide a conceptual model of centromeric heterochromatin in fission yeast that integrates our current understanding of the competing forces of transcription, replication, and RNA decay that influence its assembly and propagation.

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Section: How Conserved Is the Process Of Heterochromatin Assembly At mentioning

confidence: 99%

Centromeric heterochromatin assembly in fission yeast—balancing transcription, RNA interference and chromatin modification

2012

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“…First discovered in the tammar [15], crasiRNAs were hypothesized to be derived from mobile elements resident within centromeres [18]. Our analyses represent the first full annotation of small RNAs in this class range and have identified several salient characteristics that demarcate this class from other small RNAs (reviewed in [42]).…”

Section: Discussionmentioning

confidence: 87%

“…However, little is known about the biogenesis or sequence composition of these small RNAs. It is hypothesized that crasiRNAs emanate from both centromeric and euchromatic locations in the genome and may be involved in centromere specific histone recruitment [16,18]. …”

Section: Introductionmentioning

confidence: 99%

Unique small RNA signatures uncovered in the tammar wallaby genome

et al. 2012

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BackgroundSmall RNAs have proven to be essential regulatory molecules encoded within eukaryotic genomes. These short RNAs participate in a diverse array of cellular processes including gene regulation, chromatin dynamics and genome defense. The tammar wallaby, a marsupial mammal, is a powerful comparative model for studying the evolution of regulatory networks. As part of the genome sequencing initiative for the tammar, we have explored the evolution of each of the major classes of mammalian small RNAs in an Australian marsupial for the first time, including the first genome-scale analysis of the newest class of small RNAs, centromere repeat associated short interacting RNAs (crasiRNAs).ResultsUsing next generation sequencing, we have characterized the major classes of small RNAs, micro (mi) RNAs, piwi interacting (pi) RNAs, and the centromere repeat associated short interacting (crasi) RNAs in the tammar. We examined each of these small RNA classes with respect to the newly assembled tammar wallaby genome for gene and repeat features, salient features that define their canonical sequences, and the constitution of both highly conserved and species-specific members. Using a combination of miRNA hairpin predictions and co-mapping with miRBase entries, we identified a highly conserved cluster of miRNA genes on the X chromosome in the tammar and a total of 94 other predicted miRNA producing genes. Mapping all miRNAs to the tammar genome and comparing target genes among tammar, mouse and human, we identified 163 conserved target genes. An additional nine genes were identified in tammar that do not have an orthologous miRNA target in human and likely represent novel miRNA-regulated genes in the tammar. A survey of the tammar gonadal piRNAs shows that these small RNAs are enriched in retroelements and carry members from both marsupial and tammar-specific repeat classes. Lastly, this study includes the first in-depth analyses of the newly discovered crasiRNAs. These small RNAs are derived largely from centromere-enriched retroelements, including a novel SINE.ConclusionsThis study encompasses the first analyses of the major classes of small RNAs for the newly completed tammar genome, validates preliminary annotations using deep sequencing and computational approaches, and provides a foundation for future work on tammar-specific as well as conserved, but previously unknown small RNA progenitors and targets identified herein. The characterization of new miRNA target genes and a unique profile for crasiRNAs has allowed for insight into multiple RNA mediated processes in the tammar, including gene regulation, species incompatibilities, centromere and chromosome function.

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“…Recent work uncovering a link between LINE transcription and CENP-A deposition within a neocentromere in human supports this association (Chueh et al, 2009). However, the role of retrotransposons and RNA in endogenous mammalian centromeres remains poorly understood (but see Dawe, 2003;O'Neill and Carone, 2009). A novel class of small RNA (35-42nt, crasi RNAs, see Table 1) has been uncovered in mammals that is derived from retroelements found within CENP-A nucleosomes (Renfree et al, 2011).…”

Section: Links Between Ncrna and Chromosomal Domains Centromeresmentioning

confidence: 98%

Making a long story short: noncoding RNAs and chromosome change

2011

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As important as the events that influence selection for specific chromosome types in the derivation of novel karyotypes, are the events that initiate the changes in chromosome number and structure between species, and likewise polymorphisms, variants and disease states within species. Although once thought of as transcriptional 'noise', noncoding RNAs (ncRNAs) are now recognized as important mediators of epigenetic regulation and chromosome stability. Here we highlight recent work that illustrates the influence short and long ncRNAs have as participants in the function and stability of chromosome regions such as centromeres, telomeres, evolutionary breakpoints and fragile sites. We summarize recent evidence that ncRNAs can facilitate chromosome change and present mechanisms by which ncRNAs create DNA breaks. Finally, we present hypotheses on how they may create novel karyotypes and thus affect chromosome evolution.

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The Role of ncRNA in Centromeres: A Lesson from Marsupials

Cited by 21 publications

References 103 publications

Centromeric heterochromatin assembly in fission yeast—balancing transcription, RNA interference and chromatin modification

Centromeric heterochromatin assembly in fission yeast—balancing transcription, RNA interference and chromatin modification

Unique small RNA signatures uncovered in the tammar wallaby genome

Making a long story short: noncoding RNAs and chromosome change

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